3RIN | pdb_00003rin

p38 kinase crystal structure in complex with small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb3RIN/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-14 Released: 2012-02-29
Deposition Author(s): Segarra, V., Eastwood, P., Roca, R., Fisher, M., Lamers, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.308 (Depositor), 0.311 (DCC)
R-Value Work:
0.261 (Depositor), 0.252 (DCC)
R-Value Observed:
0.265 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Indolin-2-one p38(alpha) inhibitors I: design, profiling and crystallographic binding mode.

Eastwood, P., Gonzalez, J., Gomez, E., Vidal, B., Caturla, F., Roca, R., Balague, C., Orellana, A., Dominguez, M.

(2011) Bioorg Med Chem Lett 21: 4130-4133

PubMed: 21696951 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.05.114
Primary Citation Related Structures:
3RIN

PubMed Abstract:
The use of structure-based design and molecular modeling led to the discovery of indolin-2-one derivatives as potent and selective p38α inhibitors. The predicted binding mode was confirmed by X-ray crystallography.

Organizational Affiliation

Almirall Research Center, Almirall S.A., Ctra. Laureà Miró 408, E-08980 St. Feliu de Llobregat, Barcelona, Spain. paul.eastwood@almirall.com

Macromolecule Content

Total Structure Weight: 41.7 kDa
Atom Count: 2,939
Modeled Residue Count: 349
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0 Gene Names: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539 Go to UniProtKB: Q16539
PHAROS: Q16539 GTEx: ENSG00000112062
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I2O Query on I2O Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-cyclopropyl-4-methyl-3-(2'-oxo-1',2'-dihydrospiro[cyclopentane-1,3'-indol]-6'-yl)benzamide C₂₃ H₂₄ N₂ O₂ WMXJYEDCJIDCNY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.308 (Depositor), 0.311 (DCC)
R-Value Work: 0.261 (Depositor), 0.252 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.11	α = 90
b = 86.62	β = 90
c = 123.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description